Add Xmx option to use allocated memory more efficiently

NBISweden · Nov 14, 2023 · 329807f · 329807f
1 parent 11df9ed
commit 329807f
Showing 1 changed file with 4 additions and 2 deletions.
diff --git a/workflow/rules/3.1_bam_rmdup_realign_indels.smk b/workflow/rules/3.1_bam_rmdup_realign_indels.smk
@@ -516,7 +516,8 @@ rule indel_realigner_targets:
         "docker://broadinstitute/gatk3:3.7-0"
     shell:
         """
-        java -jar /usr/GenomeAnalysisTK.jar -T RealignerTargetCreator -R {input.ref} -I {input.bam} -o {output.target_list} -nt {threads} 2> {log}
+        mem=$(((6 * {threads}) - 2))
+        java -jar -Xmx${{mem}}g /usr/GenomeAnalysisTK.jar -T RealignerTargetCreator -R {input.ref} -I {input.bam} -o {output.target_list} -nt {threads} 2> {log}
         """
 
 
@@ -538,7 +539,8 @@ rule indel_realigner:
         "docker://broadinstitute/gatk3:3.7-0"
     shell:
         """
-        java -jar /usr/GenomeAnalysisTK.jar -T IndelRealigner -R {input.ref} -I {input.bam} -targetIntervals {input.target_list} -o {output.realigned} 2> {log}
+        mem=$(((6 * {threads}) - 2))
+        java -jar -Xmx${{mem}}g /usr/GenomeAnalysisTK.jar -T IndelRealigner -R {input.ref} -I {input.bam} -targetIntervals {input.target_list} -o {output.realigned} 2> {log}
         """